Update examples and format notes in Jupyter notebook examples

src/docs/doc_tokamaker_main.md

@@ -17,10 +17,12 @@ The following examples illustrate usage of TokaMaker to compute different Grad-S
 
 ### Mesh Generation
  - \subpage doc_tMaker_mesh_ex1
+ - \subpage doc_tMaker_mesh_ex2
 
 ### Fixed Boundary Equilibria
  - \subpage doc_tMaker_ex1
  - \subpage doc_tMaker_ex2
 
 ### Free Boundary Equilibria
- - \subpage doc_tMaker_ex3
+ - \subpage doc_tMaker_ex3
+ - \subpage doc_tMaker_ex4

src/examples/TokaMaker/ITER/ITER_mesh_ex.ipynb

@@ -121,12 +121,16 @@
     " - `vv2`: The outer vacuum vessel\n",
     " - `PF1,...`: Each of the 14 coils in ITER (6 CS, 6 PF, 2 VS)\n",
     "\n",
+    "In ITER all coils are independent except for the vertical stability coil (`VS`), which is single coil set composed of two counter-wound coils. To treat this set as a single coil we use the `coil_set` and `nTurns` argument to \\ref OpenFUSIONToolkit.TokaMaker.gs_Domain.define_region \"define_region()\" to join the coils in a single `VS` coil set with opposing polarities.\n",
+    "\n",
+    "**Note:** `nTurns` can also be used to define the number of turns in a given coil region. At the moment we are not including # of turns in this model so we keep the amplitude for each coil as 1.0 and only adjust the polarity.\n",
+    "\n",
     "For each region you can provide a target size and one of four region types:\n",
     " - `plasma`: The region where the plasma can exist and the classic Grad-Shafranov equation with $F*F'$ and $P'$ are allowed. **There can only be one region of this type**\n",
     " - `vacuum`: A region where not current can flow and $\\nabla^* \\psi = 0$ is solved\n",
     " - `boundary`: A special case of the `vacuum` region, which forms the outer boundary of the computational domain. **A region of this type is required if more than one region is specified**\n",
     " - `conductor`: A region where toroidal current can flow passively (no externally applied voltage). For this type of region the resistivity should be specified with the argument `eta` in units of $\\omega \\mathrm{-m}$.\n",
-    " - `coil`: A region where toroidal current can flow with specified amplitude through \\ref OpenFUSIONToolkit.TokaMaker.TokaMaker.set_coil_currents or via shape optimization \\ref OpenFUSIONToolkit.TokaMaker.TokaMaker.set_coil_reg and \\ref OpenFUSIONToolkit.TokaMaker.TokaMaker.set_isoflux"
+    " - `coil`: A region where toroidal current can flow with specified amplitude through \\ref OpenFUSIONToolkit.TokaMaker.TokaMaker.set_coil_currents \"set_coil_currents()\" or via shape optimization \\ref OpenFUSIONToolkit.TokaMaker.TokaMaker.set_coil_reg \"set_coil_reg()\" and \\ref OpenFUSIONToolkit.TokaMaker.TokaMaker.set_isoflux \"set_isoflux()\""
    ]
   },
   {
@@ -161,8 +165,8 @@
     "## Define geometry for region boundaries\n",
     "Once the region types and properties are defined we now define the geometry of the mesh using shapes and references to the defined regions.\n",
     " 1. We add the limiter contour as a \"polygon\", referencing `plasma` as the region enclosed by the contour and `vacuum1` as the region outside the contour.\n",
-    " 2. We add the inner vacuum as an \"annulus\" with curves defining the inner and outer edges respectively. We also reference `vacuum1` as the region enclosed by the annulus, `vv1` as the annular region itself, and `vacuum2` as the region outside the annulus.\n",
-    " 3. We add the outer vacuum as an \"annulus\" with curves defining the inner and outer edges respectively. We also reference `vacuum2` as the region enclosed by the annulus, `vv2` as the annular region itself, and `air` as the region outside the annulus.\n",
+    " 2. We add the inner vacuum vessel as an \"annulus\" with curves defining the inner and outer edges respectively. We also reference `vacuum1` as the region enclosed by the annulus, `vv1` as the annular region itself, and `vacuum2` as the region outside the annulus.\n",
+    " 3. We add the outer vacuum vessel as an \"annulus\" with curves defining the inner and outer edges respectively. We also reference `vacuum2` as the region enclosed by the annulus, `vv2` as the annular region itself, and `air` as the region outside the annulus.\n",
     " 4. We add each of the 14 coils as \"rectangles\", which are defined by a center point (R,Z) along with a width (W) and height (H). We also reference `air` as the region outside the rectangle for the CS and PF coils and `vacuum1` for the VS coils."
    ]
   },
@@ -237,7 +241,7 @@
    "metadata": {},
    "source": [
     "## Create mesh\n",
-    "Now we generate the actual mesh using the \\ref OpenFUSIONToolkit.TokaMaker.gs_Domain.build_mesh \"build_mesh\" method. Additionally, if `coil` and/or `conductor` regions are defined the \\ref OpenFUSIONToolkit.TokaMaker.gs_Domain.get_coils \"get_coils\" and \\ref OpenFUSIONToolkit.TokaMaker.gs_Domain.get_conductors \"get_conductors\" methods should also be called to get descriptive dictionaries for later use in TokaMaker. This step may take a few moments as [triangle](https://www.cs.cmu.edu/~quake/triangle.html) generates the mesh.\n",
+    "Now we generate the actual mesh using the \\ref OpenFUSIONToolkit.TokaMaker.gs_Domain.build_mesh \"build_mesh()\" method. Additionally, if `coil` and/or `conductor` regions are defined the \\ref OpenFUSIONToolkit.TokaMaker.gs_Domain.get_coils \"get_coils()\" and \\ref OpenFUSIONToolkit.TokaMaker.gs_Domain.get_conductors \"get_conductors()\" methods should also be called to get descriptive dictionaries for later use in TokaMaker. This step may take a few moments as [triangle](https://www.cs.cmu.edu/~quake/triangle.html) generates the mesh.\n",
     "\n",
     "Note that, as is common with unstructured meshes, the mesh is stored a list of points `mesh_pts` of size (np,2), a list of cells formed from three points each `mesh_lc` of size (nc,3), and an array providing a region id number for each cell `mesh_reg` of size (nc,), which is mapped to the names above using the `coil_dict` and `cond_dict` dictionaries."
    ]
@@ -324,7 +328,7 @@
    "metadata": {},
    "source": [
     "## Save mesh for later use\n",
-    "As generation of the mesh often takes comparable, or longer, time compare to runs in TokaMaker it is useful to separate generation of the mesh into a different script as demonstrated here. The method \\ref OpenFUSIONToolkit.TokaMaker.save_gs_mesh can be used to save the resulting information for later use. This is done using and an [HDF5](https://www.hdfgroup.org/solutions/hdf5/) file through the [h5py](https://www.h5py.org/) library."
+    "As generation of the mesh often takes comparable, or longer, time compare to runs in TokaMaker it is useful to separate generation of the mesh into a different script as demonstrated here. The method \\ref OpenFUSIONToolkit.TokaMaker.save_gs_mesh \"save_gs_mesh()\" can be used to save the resulting information for later use. This is done using and an [HDF5](https://www.hdfgroup.org/solutions/hdf5/) file through the [h5py](https://www.h5py.org/) library."
    ]
   },
   {

src/utilities/generate_doc.py

@@ -176,6 +176,8 @@ def parse_fortran_file(fid):
         # Update image paths
         contents = contents.replace("{0}_files".format(file_name), "images")
         contents = contents.replace("[png]", "[]")
+        # Convert notes to note blocks
+        contents = contents.replace("**Note:**", r'@note')
         # Convert code block style
         contents_split = contents.split('```')
         for i, content_segment in enumerate(contents_split):